I don’t know about the status of Snaps nowadays, but Flatpaks tend to adapt to the theme of the app. Spotify, for instance, uses a dark topbar in Adwaita, even if the theme is light. Cp. for instance some of GNOME’s core apps, like Video and Weather.
I assume the new Yaru theme is also going to have this feature.
Aside from that, there is talk of three variants making their way to the Adwaita theme: the default light theme, the existing dark one, and an in-between ‘darker’ variant. Each of which brands like Ubuntu or Pop_OS will be free to brand/modify.
So, don’t worry, dark header bars are going to come back, and in the meantime, look out for differences between core apps, Snaps and Flatpaks.